IOCBIO Kinetics: An open-source software solution for analysis of data traces

Vendelin, Marko; Laasmaa, Martin; Kalda, Mari; Branovets, Jelena; Karro, Niina; Barsunova, Karina; Birkedal, Rikke

doi:10.1371/journal.pcbi.1008475

Cited by 4 publications

(4 citation statements)

References 16 publications

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“…The database layout has been designed to simplify the usage of the software in an environment where a central database is used to keep experimental results from different types of experiments, such as when a central laboratory database is shared by multiple primary analysis tools [ 10 , 11 ] and management systems [ 12 – 15 ]. For that, we isolated the data stored by the software using PostgreSQL schema—named collection of tables and views.…”

Section: Methodsmentioning

confidence: 99%

Simple analysis of gel images with IOCBIO Gel

Kütt,

Margus,

Kask

et al. 2023

BMC Biol

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Background Current solutions for the analysis of Western Blot images lack either transparency and reproducibility or can be tedious to use if one has to ensure the reproducibility of the analysis. Results Here, we present an open-source gel image analysis program, IOCBIO Gel. It is designed to simplify image analysis and link the analysis results with the metadata describing the measurements. The software runs on all major desktop operating systems. It allows one to use it in either a single-researcher environment with local storage of the data or in a multiple-researcher environment using a central database to facilitate data sharing within the research team and beyond. By recording the original image and all operations performed on it, such as image cropping, subtraction of background, sample lane selection, and integration boundaries, the software ensures the reproducibility of the analysis and simplifies making corrections at any stage of the research. The analysis results are available either through direct access to the database used to store it or through the export of the relevant data. Conclusions The software is not only limited to Western Blot image analysis and can be used to analyze images obtained as a part of many other widely used biochemical techniques such as isoelectric focusing. By recording the original data and all the analysis steps, the program improves reproducibility in the analysis and contributes to the implementation of FAIR principles in the related fields.

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Section: Methodsmentioning

confidence: 99%

Simple analysis of gel images with IOCBIO Gel

Kütt,

Margus,

Kask

et al. 2023

BMC Biol

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“…The background intensity from the separately recorded image was determined using ImageJ. Ca 2+ transients were analysed by IOCBIO Kinetics open‐source software after manually marking each Ca 2+ transient (Vendelin et al., 2020). In this analysis, Ca 2+ transients were fitted by monotonic cubic interpolation, and transient properties, such as amplitude, duration at half‐maximum and time‐moments at which transient reached half‐maximum values were determined.…”

Section: Methodsmentioning

confidence: 99%

“…Analysis was performed using scripts from IOCBIO Kinetics (Vendelin et al., 2020). Additional SQL and Python scripts were written to fetch the data from the database and used as an input for R statistical analysis scripts.…”

Section: Methodsmentioning

confidence: 99%

Cardiomyocytes from female compared to male mice have larger ryanodine receptor clusters and higher calcium spark frequency

Laasmaa,

Branovets,

Stolova

et al. 2023

The Journal of Physiology

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Sex differences in cardiac physiology are receiving increased attention as it has become clear that men and women have different aetiologies of cardiac disease and require different treatments. There are experimental data suggesting that male cardiomyocytes exhibit larger Ca2+ transients due to larger Ca2+ sparks and a higher excitation–contraction coupling gain; in addition, they exhibit a larger response to adrenergic stimulation with isoprenaline (ISO). Here, we studied whether there are sex differences relating to structural organization of the transverse tubular network and ryanodine receptors (RyRs). Surprisingly, we found that female cardiomyocytes exhibited a higher spark frequency in a range of spark magnitudes. While overall RyR expression and phosphorylation were the same, female cardiomyocytes had larger but fewer RyR clusters. The density of transverse t‐tubules was the same, but male cardiomyocytes had more longitudinal t‐tubules. The Ca2+ transients were similar in male and female cardiomyocytes under control conditions and in the presence of ISO. The synchrony of the Ca2+ transients was similar between sexes as well. Overall, our data suggest subtle sex differences in the Ca2+ influx and efflux pathways and their response to ISO, but these differences are balanced, resulting in similar Ca2+ transients in field‐stimulated male and female cardiomyocytes. The higher spark frequency in female cardiomyocytes is related to the organization of RyRs into larger, but fewer clusters. imageKey points During a heartbeat, the force of contraction depends on the amplitude of the calcium transient, which in turn depends on the amount of calcium released as calcium sparks through ryanodine receptors in the sarcoplasmic reticulum. Previous studies suggest that cardiomyocytes from male compared to female mice exhibit larger calcium sparks, larger sarcoplasmic reticulum calcium release and greater response to adrenergic stimulation triggering a fight‐or‐flight response. In contrast, we show that cardiomyocytes from female mice have a higher spark frequency during adrenergic stimulation and similar spark morphology. The higher spark frequency is related to the organization of ryanodine receptors into fewer, but larger clusters in female compared to male mouse cardiomyocytes. Despite subtle sex differences in cardiomyocyte structure and calcium fluxes, the differences are balanced, leading to similar calcium transients in cardiomyocytes from male and female mice.

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“…All enzyme activity measurements were performed in triplicate (in quadruplicate for CO) and the results averaged. Data was analysed using IOCBIO Kinetics [83].…”

Section: Enzyme Activitiesmentioning

confidence: 99%

Rat and mouse cardiomyocytes show subtle differences in creatine kinase expression and compartmentalization

Branovets,

Soodla,

Vendelin

et al. 2023

PLoS ONE

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Creatine kinase (CK) and adenylate kinase (AK) are energy transfer systems. Different studies on permeabilized cardiomyocytes suggest that ADP-channelling from mitochondrial CK alone stimulates respiration to its maximum, VO2_max, in rat but not mouse cardiomyocytes. Results are ambiguous on ADP-channelling from AK to mitochondria. This study was undertaken to directly compare the CK and AK systems in rat and mouse hearts. In homogenates, we assessed CK- and AK-activities, and the CK isoform distribution. In permeabilized cardiomyocytes, we assessed mitochondrial respiration stimulated by ADP from CK and AK, VO2_CK and VO2_AK, respectively. The ADP-channelling from CK or AK to mitochondria was assessed by adding PEP and PK to competitively inhibit the respiration rate. We found that rat compared to mouse hearts had a lower aerobic capacity, higher VO2_CK/VO2_max, and different CK-isoform distribution. Although rat hearts had a larger fraction of mitochondrial CK, less ADP was channeled from CK to the mitochondria. This suggests different intracellular compartmentalization in rat and mouse cardiomyocytes. VO2_AK/VO2_max was similar in mouse and rat cardiomyocytes, and AK did not channel ADP to the mitochondria. In the absence of intracellular compartmentalization, the AK- and CK-activities in homogenate should have been similar to the ADP-phosphorylation rates estimated from VO2_AK and VO2_CK in permeabilized cardiomyocytes. Instead, we found that the ADP-phosphorylation rates estimated from permeabilized cardiomyocytes were 2 and 9 times lower than the activities recorded in homogenate for CK and AK, respectively. Our results highlight the importance of energetic compartmentalization in cardiac metabolic regulation and signalling.

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IOCBIO Kinetics: An open-source software solution for analysis of data traces

Cited by 4 publications

References 16 publications

Simple analysis of gel images with IOCBIO Gel

Simple analysis of gel images with IOCBIO Gel

Cardiomyocytes from female compared to male mice have larger ryanodine receptor clusters and higher calcium spark frequency

Rat and mouse cardiomyocytes show subtle differences in creatine kinase expression and compartmentalization

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